Several classes of viruses form stable associations with their hosts by the integration of one or more copies of the viral genome into host cell DNA. Retroviruses provide a unique and important system for the study of integrative recombination since exogenously acquired genomes are integrated with high efficiency at a specific site in the viral genome, but at a large number of sites in the host chromosome. Molecular clones of several newly integrated retroviral genomes were produced in either plasmid or bacteriophage cloning vehicles using approved recombinant DNA techniques and were characterized using electron microscope heteroduplex and R-looping methods. These studies have not only provided information on the structural arrangement of both integrated viral and flanking cellular sequences but also have confirmed the presence of transformation specific sequences in normal, uninfected host cells. The major objective of these studies has been the application of physical and biochemical techniques to assess the influence of flanking cellular sequences on subsequent viral function and to define in molecular terms those events which take place during integrative recombination.